validate_input_files: Verify that the input taxon_table file and the input mapping...
In gauravsk/ranacapa: Utility Functions and 'shiny' App for Simple Environmental DNA Visualizations and Analyses
Description
Usage
Arguments
Examples
Description
Verify that the input taxon_table file and the input mapping file meets specificationss
The function takes one taxon table as its input, and verfies that it meets
the expected standards.
The standards incude:
1. Column names exist.
2. One of the columns is named "sum.taxonomy"
3. The "xxx_seq_number" column, if it ever existed, is removed
4. All columns apart from sum.taxonomy should be numeric
5. All columns apart from sum.taxonomy should have corresponding row in metadata file
Usage
1
validate_input_files(taxon_table, metadata_file)
Arguments
taxon_table
taxonomy table from Anacapa
metadata_file
Qiime-style mapping
Examples
1
2
3
4
5
good_taxon_table <- data.frame(sum.taxonomy = c("a;b;c;d;f;u", "p;q;r;s;t;u"),
site_1 = c(0,1), site_2 = c(10, 20))
good_maps <- data.frame(site = c("site_1", "site_2"),
season = c("wet", "dry"), host = c("oak", "sage"))
validate_input_files(good_taxon_table, good_maps)
gauravsk/ranacapa documentation built on June 7, 2019, 4:03 a.m.
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Description Usage Arguments Examples
Description
Verify that the input taxon_table file and the input mapping file meets specificationss The function takes one taxon table as its input, and verfies that it meets the expected standards. The standards incude: 1. Column names exist. 2. One of the columns is named "sum.taxonomy" 3. The "xxx_seq_number" column, if it ever existed, is removed 4. All columns apart from sum.taxonomy should be numeric 5. All columns apart from sum.taxonomy should have corresponding row in metadata file
Usage
1 | validate_input_files(taxon_table, metadata_file)
|
Arguments
taxon_table |
taxonomy table from Anacapa |
metadata_file |
Qiime-style mapping |
Examples
1 2 3 4 5 | good_taxon_table <- data.frame(sum.taxonomy = c("a;b;c;d;f;u", "p;q;r;s;t;u"),
site_1 = c(0,1), site_2 = c(10, 20))
good_maps <- data.frame(site = c("site_1", "site_2"),
season = c("wet", "dry"), host = c("oak", "sage"))
validate_input_files(good_taxon_table, good_maps)
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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